A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/transcriptassembler analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2025-02-20, 16:45 UTC
based on data in:
/home/esteban/projects/nf-core-transcriptassembler/work/b6/9ce16333b4cdd5ef98ea4ab8326460
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| BUSCO | busco | 5.5.0 |
| DIAMOND_BLASTP | diamond | 2.0.15 |
| DIAMOND_MAKEDB | diamond | 2.0.15 |
| FASTQC_RAW | fastqc | 0.12.1 |
| TRANSDECODER_LONGORF | transdecoder | 5.7.1 |
| TRANSDECODER_PREDICT | transdecoder_predict | 5.7.1 |
| TRINITY | trinity | 2.13.2) |
| Workflow | Nextflow | 24.10.4 |
| nf-core/transcriptassembler | v.1.0.14dev |
nf-core/transcriptassembler Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/transcriptassembler
Methods
Data was processed using nf-core/transcriptassembler vv.1.0.14dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v24.10.4 (Di Tommaso et al., 2017) with the following command:
nextflow run main.nf -profile test,docker --outdir test_out
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/transcriptassembler Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/transcriptassembler
RNA assembly QC (BUSCO)
- busco_lineage_path
- /home/esteban/projects/nf-core-transcriptassembler/assets/busco_test_data
Input/output options
- input
- /home/esteban/projects/nf-core-transcriptassembler/assets/samplesheet_test.csv
- outdir
- test_out
Institutional config options
- config_profile_description
- Minimal test dataset to check pipeline function
- config_profile_name
- Test profile
Core Nextflow options
- configFiles
- N/A
- containerEngine
- docker
- launchDir
- /home/esteban/projects/nf-core-transcriptassembler
- profile
- test,docker
- projectDir
- /home/esteban/projects/nf-core-transcriptassembler
- runName
- suspicious_engelbart
- userName
- esteban
- workDir
- /home/esteban/projects/nf-core-transcriptassembler/work